I'm not sure that this is a CQR problem, but...
Very often, when I start CQR, the WK1EL keyer is not connected, or more exactly, the USB port is not always the one of the previous session.
So with a "ls /dev/tty*", I check the used ports, and I change it in the preference panel, and everything is working fine, but this is annoying.
Strangely, the link to the rig is stable. I had a problem once, but it was solved by a restart of Linux.
For info, I'm with Debian Jessie, and CQR 1.8.2.
Thanks in advance for any hint.